


Silver Linings

by StarSparkle2403



Category: Iron Man (Movies), Marvel Cinematic Universe, Spider-Man: Homecoming (2017), The Avengers (Marvel Movies)
Genre: Alpha/Beta/Omega Dynamics, Cuddling & Snuggling, Fluff, Not Canon Compliant, Peter's Having a Bad Day, Tony Tries to Help
Language: English
Status: Completed
Published: 2019-05-04
Updated: 2019-06-20
Packaged: 2020-02-23 18:45:46
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 2
Words: 1,714
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/18707815
Author URL: https://archiveofourown.org/users/StarSparkle2403/pseuds/StarSparkle2403
Summary: Peter's not having a good day, and it may have just gotten worse.Or did it?





	1. Chapter 1

**Author's Note:**

> I seem to have a weak spot for Omega! Peter not knowing what the hell is going on.

Peter was having a bad day.

First he got a B on his History test (which dropped his grade to an A-), then he realised that he forgot his phone at home, he was late for his time with Mr. Stark, he still had to go on patrol that night even though he had a crap ton of homework, and, on top of that, he had a killer headache.

“Your heart rate seems much too high for someone your age and body composition,” JARVIS said worriedly when Peter stepped into the elevator. “Perhaps you should take a few deep breaths?”

“I don't have time for that,” Peter said, bouncing on his toes. “I'm late.”

“Given how many times Sir has been late, I don't think he would mind,” JARVIS replied as the doors slid open.

“Hey, Pete!” Mr. Stark said cheerily. “How was school?”

“Horrible,” Peter muttered, dropping his backpack next to his personal workbench and sitting down in his chair. He rubbed his temples, trying to will his headache away.

Mr. Stark rolled over in his wheelie chair, a frown on his face. “What’s up?” he asked. “A bad day doesn’t usually make you this upset.”

“Nothing’s up,” Peter said, turning to the holographic screen and pulling up the project he was working on.

“I don’t believe that,” Mr. Stark said, wheeling closer. “Come on, kid. Out with it.”

“I’m fine,” Peter insisted, shoulders tensing up defensively. Mr. Stark stared at him expectantly, one eyebrow raised. “Really, I’m okay. School is okay, home is okay, my friends are okay, everything’s okay!” Peter burst out.

“Just okay?” Mr. Stark asked.

Peter looked up at him, shocked. Everything was just okay. Not good, not bad, just okay. Against his will, his eyes filled with tears.

“Come here,” Mr. Stark said, holding his arms out. Peter scooted forward and leaned against his chest. Mr. Stark wrapped his arms around him and held him close.

Peter sighed as Mr. Stark’s scent wrapped around him. Never before had he been so happy that Mr. Stark often let his scent blockers wear off while he was working.

“Are you sniffing me?” Mr. Stark asked, sounding amused.

Peter snuggled closer, gripping the man’s shirt. “Yeah,” he said. “You smell nice.”

There was a pause before Mr. Stark said, “What do I smell like?”

“Fire and metal,” Peter replied. “And sweet like flowers.” He sniffed. “Jasmine? No, honeysuckle.”

Mr. Stark pulled away and looked down at him. “Pete, what’s your designation again?”

“Beta, why?”

***

“May, what designations were Peter’s parents?”

“They were both Betas. Why do you ask?”

“Because I don’t think Peter is.”

Tony could practically hear May’s eyebrow raise through the phone. “That’s impossible. You and I both know that perfectly well. Two Beta parents can’t give birth to an Alpha or Omega child.”

“I know that,” Tony said, looking over to the couch where Peter was taking a nap. “But he just told me what every person on the team smelled like, and he didn’t make one error.”

“That’s odd,” May conceded. “But he could just have a really good sense of smell.”

Tony sighed. “Maybe,” he said. “I’m having Bruce run some tests just to be sure.”

***

“Well, Tony, looks like you were right,” Bruce said, showing him the test results. “Peter is definitely an Omega. The question is how.”

Tony flipped through the results. “I don’t know Brucie. All I can think of is that maybe one of his parents isn’t his parent.” 

“I can run a DNA test,” Bruce suggested quietly. “Just to make sure. We wouldn’t have to tell anyone we did it if his parents are who he thinks they are.”

“I don’t want to invade his privacy like that.” Tony sighed, running a hand down his face.

“We might have to,” Bruce replied. “We don't want to risk his physical health if there’s any diseases or conditions that a parent could have passed down to him.”

“I don't want to risk his mental health either,” Tony said. “But it would be great if we could find another Omega in his family to help him relax.”

***

Peter didn't know what Mr. Stark and Doctor Banner were talking about, but from the looks on their faces, it wasn't anything good.

Mr. Stark turned, a StarkPad in his hands, and walked over to Peter. “I have some news for you,” he said, sitting down next to Peter. His scent was edged with the sharp tang of nervousness.

“What is it?” Peter asked warily.

Mr. Stark looked down at the StarkPad, then back up at him. “Bruce ran a couple tests, and it turns out that you’re not a Beta.”

Peter stared at him. “What?” he asked, very confused. “I can't be. Both my parents were Betas.” 

Mr. Stark cleared his throat awkwardly. “We were wondering about that too, so we ran a DNA test,” he said. He stopped, clearly uncomfortable.

When Mr. Stark didn't go on, Peter scooted closer and rested his head on the man’s shoulder, trying to see the results on the StarkPad’s screen.

What he saw changed everything.

~

Peter Benjamin Parker

Designation:  
Omega

Guardian:  
May Parker (Not Blood Related)

Parents:  
Mary Parker née Fitzpatrick (Deceased); Anthony Edward Stark (Alive)

~

“W-what?” Peter pulled away and looked up at Mr. Stark. “Did you know?”

Mr. Stark shook his head. “I didn’t,” he replied, “but I wish I had.” He smiled weakly. “Now come give me a hug before I start crying.”

***

Peter didn’t know what to do. Everything he thought he knew was wrong.

He wasn’t ever a Beta, his father wasn’t his father, and now he finds out that he has a very high chance of dying.

“Breathe.” A warm hand landed on the back of his neck. 

Peter took a shaky breath and buried his nose in the man’s neck. Antiseptic and herbs.

“That’s it,” the man said gently. “We were getting worried for a minute there.” He petted Peter’s hair. “Especially Tony.”

Peter pulled back to look at him. “Is he okay?” he asked worriedly.

“He’s fine, just went to get some blankets,” Doctor Banner said, sitting down next to him and handing his a glass of water.

“Thanks,” Peter said quietly before taking a drink, hands shaking. He looked up at Doctor Banner. “Is Mr. Stark going to be back soon?”

Doctor Banner smiled kindly. “I’m sure he will,” he replied. “He didn’t want to leave in the first place.”


	2. Chapter 2

Mr. Stark burst back into the lab a few minutes later, arms laden with blankets. “Pete!” he said, walking toward the back wall. “Come with me.”

Peter looked at Doctor Banner questioningly, but the man just shrugged. “You better go,” he said, standing up. “I have to get back to work anyway.”

“Okay,” Peter replied, standing as well and giving him a hug. “I’ll see you later right?”

Doctor Banner hugged him back gently. “Of course.” 

Peter let him go and went over to where Mr. Stark was waiting impatiently by the wall. Mr. Stark tapped on the wall twice and a section slid open. He gestured for Peter to go in, then followed him.

As the wall slid closed, Peter stopped in his tracks. “Wow,” he breathed.

“Do you like it?” Mr. Stark asked, dropping the blankets on top of the giant pile of pillows and cushions that filled the room.

“Like it?” Peter flopped down on the pile. “I love it.”

***

“Comfy?” Mr. Stark asked after a while.

“Yeah,” Peter said into the blankets.

“Well, turn over, we need to talk.”

That didn’t sound good. Peter flipped over onto his back and looked over at where Mr. Stark was lounging. “What is it?” he asked nervously.

“There are some things you need to know about being an Omega,” Mr. Stark said kindly.

Peter stared at hi for a second. “Is this going to be as uncomfortable as I think it will be?”

“Probably,” Mr. Stark said cheerily. He tossed a small box to Peter and said, “Put those on your neck, please.”

Peter opened the box and put the two patches that were inside on both sides of his neck. “What’s this for, Mr. Stark?”

“One, just call me Tony, and two,” he pulled out his phone, “they are going to read your hormone levels so that we can figure out how to stabilize them.”

“I didn’t know that they had to be,” Peter replied, fidgeting with the edge of a blanket.

“You wouldn’t,” Mr. Sta- Tony said, tapping away. “A doctor wouldn’t have a reason to test them unless they knew you were an Omega.”

Peter flipped over onto his back and looked at him upside down. “Why didn’t anyone know?”

“Everyone thought that both your parents were Betas, and two Betas can’t give birth to an Alpha or Omega,” Tony replied, then frowned. “You look a bit off,” he said. He looked a little uncomfortable.

“How do we fix it?” Peter asked anxiously. “Do I have to take pills? Please don’t say I have to have a shot.”

“You don’t have to have a shot.”

“Oh, thank God.”

Tony smiled. “It’s actually a lot easier than you would think.” He opened his arms. “Come here.”

Peter’s eyes lit up. “I finally get a hug?”

“Yep. Now come on, don’t leave me hanging.”

Peter crawled over and flopped onto Tony. “This is nice,” he said. “Is this all we do?” Tony nodded. “Okay. I can do that.” He snuggled closer happily.

After a few minutes, Peter asked, “Why does this work?”

“Pheromones,” Tony replied. Peter lifted his head and raised an eyebrow. “Your body responds to the pheromones in my scent and levels out your hormones to a safe degree.”

“A safe degree?” Peter asked, eyes wide. “What do you mean? Am I sick? Am I going to die? I don’t want to die!”

“Shh,” Tony soothed, pressing Peter’s nose to the scent gland on his neck. “You’re fine. Your hormone levels weren’t nearly as bad as I thought they would be, and they were a long way off from making you sick.”

“Okay,” Peter said quietly, trying to relax.

“But,” Tony continued. “If you ever feel off, just tell me, and we’ll fix it.”

Peter nodded. “I will.”

Tony smiled and pulled his newfound son closer.


End file.
